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60-534: Thaliacea is a class of marine chordates within the subphylum Tunicata , comprising the salps , pyrosomes and doliolids . Unlike their benthic relatives the ascidians , from which they are believed to have emerged, thaliaceans are free-floating ( pelagic ) for their entire lifespan. The group includes species with complex life cycles, with both solitary and colonial forms. The three orders of thaliaceans are filter feeders . Pyrosomes are colonial animals, with multiple tiny ascidian -like zooids arranged in

120-402: A cartilaginous / bony axial endoskeleton ( spine ) and are cladistically and phylogenetically a subgroup of the clade Craniata (i.e. chordates with a skull ); Tunicata or Urochordata ( sea squirts , salps , and larvaceans ), which only retain the synapomorphies during their larval stage; and Cephalochordata ( lancelets ), which resemble jawless fish but have no gills or

180-443: A 2 aa deletion in leucyl-tRNA synthetase was commonly present in the above orders of the class Gammaproteobacteria and in some members of the order Oceanospirillales. Another CSI-based study has also identified 4 CSIs that are exclusive to the order Xanthomonadales. Taken together, these two facts show that Xanthomonadales is a monophyletic group that is ancestral to other Gammaproteobacteria, which further shows that Xanthomonadales

240-486: A conserved insert or deletion is shared by several major phyla, but absent from other phyla. Figure 2 shows an example of 5aa CSI found in a conserved region that is commonly present in the species belonging to phyla X, Y and Z, but it is absent in other phyla (A, B and C). This signature indicates a specific relationship of taxa X, Y and Z and also A, B and C. Based upon the presence or absence of such an indel, in out-group species (viz. Archaea), it can be inferred whether

300-440: A cylinder closed at one end. All of the atrial siphons point inwards, emptying into a single, common cloaca in the centre of the cylinder. As the water exhaled by the zooids exits through a common opening, the water movement slowly propels the pyrosome through the sea. Salps and doliolids have a transparent barrel-shaped body through which they pump water, propelling them through the sea, and from which they extract food. The bulk of

360-503: A detailed classification within the living chordates. Attempts to produce evolutionary " family trees " shows that many of the traditional classes are paraphyletic . Hemichordates [REDACTED] Echinoderms [REDACTED] Cephalochordates [REDACTED] Tunicates [REDACTED] Craniates ( vertebrates ) [REDACTED] While this has been well known since the 19th century, an insistence on only monophyletic taxa has resulted in vertebrate classification being in

420-429: A distinct head . The vertebrates and tunicates compose the clade Olfactores , which is sister to Cephalochordata (see diagram under Phylogeny ). Extinct taxa such as the conodonts are chordates, but their internal placement is less certain. Hemichordata (which includes the acorn worms ) was previously considered a fourth chordate subphylum, but now is treated as a separate phylum which are now thought to be closer to

480-436: A long time regarded as larvae of the other two groups. The other two groups, the sea squirts and the salps, metamorphize into adult forms which lose the notochord, nerve cord, and post anal tail. Both are soft-bodied filter feeders with multiple gill slits. They feed on plankton which they collect in their mucus. Sea squirts are sessile and consist mainly of water pumps and filter-feeding apparatus. Most attach firmly to

540-549: A new study have shown possible affinity of these Ediacaran organisms to the ascidians. Ausia and Burykhia lived in shallow coastal waters slightly more than 555 to 548 million years ago, and are believed to be the oldest evidence of the chordate lineage of metazoans. The Russian Precambrian fossil Yarnemia is identified as a tunicate only tentatively, because its fossils are nowhere near as well-preserved as those of Ausia and Burykhia , so this identification has been questioned. Fossils of one major deuterostome group,

600-429: A number of CSIs were found that are specific for different orders of Thermoproteota—3 CSIs for Sulfolobales , 5 CSIs for Thermoproteales , lastly 2 CSIs common for Sulfolobales and Desulfurococcales . The signatures described provide novel means for distinguishing Thermoproteota and Nitrososphaerota, additionally they could be used as a tool for the classification and identification of related species. The members of

660-497: A particular clade or group of species, generally provide good phylogenetic markers of common evolutionary descent. Due to the rarity and highly specific nature of such changes, it is less likely that they could arise independently by either convergent or parallel evolution (i.e. homoplasy) and therefore are likely to represent synapomorphy . Other confounding factors such as differences in evolutionary rates at different sites or among different species also generally do not affect

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720-406: A particular taxon (e.g. genus, family, class, order, phylum) but they are not present in other groups. These CSIs were most likely introduced in an ancestor of the group of species before the members of the taxa diverged. They provide molecular means for distinguishing members of a particular taxon from all other organisms. Figure 1 shows an example of 5aa CSI found in all species belonging to

780-463: A poor fossil record, attempts have been made to calculate the key dates in their evolution by molecular phylogenetics techniques—by analyzing biochemical differences, mainly in RNA. One such study suggested that deuterostomes arose before 900  million years ago and the earliest chordates around 896  million years ago . However, molecular estimates of dates often disagree with each other and with

840-617: A post- anal tail . In addition to the morphological characteristics used to define chordates, analysis of genome sequences has identified two conserved signature indels (CSIs) in their proteins: cyclophilin -like protein and inner mitochondrial membrane protease ATP23, which are exclusively shared by all vertebrates , tunicates and cephalochordates . These CSIs provide molecular means to reliably distinguish chordates from all other animals . Chordates are divided into three subphyla : Vertebrata ( fish , amphibians , reptiles , birds and mammals ), whose notochords are replaced by

900-421: A rudimentary one in some doliolid larvae. Thaliaceans play an important role in the ecology of the sea. Their dense faecal pellets sink to the bottom of the oceans, and this may be a major part of the worldwide carbon cycle . The class is a relatively small one, and is divided into three orders: Class Thaliacea Chordate And see text A chordate ( / ˈ k ɔːr d eɪ t / KOR -dayt )

960-480: A state of flux. The majority of animals more complex than jellyfish and other Cnidarians are split into two groups, the protostomes and deuterostomes , the latter of which contains chordates. It seems very likely the 555 million-year-old Kimberella was a member of the protostomes. If so, this means the protostome and deuterostome lineages must have split some time before Kimberella appeared—at least 558  million years ago , and hence well before

1020-530: A taxon comprising tunicates, cephalochordates, and vertebrates in 1866. Though he used the German vernacular form, it is allowed under the ICZN code because of its subsequent latinization. Chordates form a phylum of animals that are defined by having at some stage in their lives all of the following anatomical features: There are soft constraints that separate chordates from other biological lineages, but are not part of

1080-440: Is a deuterostomal bilaterian animal belonging to the phylum Chordata ( / k ɔːr ˈ d eɪ t ə / kor- DAY -tə ). All chordates possess, at some point during their larval or adult stages, five distinctive physical characteristics ( synapomorphies ) that distinguish them from other taxa . These five synapomorphies are a notochord , a hollow dorsal nerve cord , an endostyle or thyroid , pharyngeal slits , and

1140-457: Is absent in other ancestral bacterial phyla as well as Archaea . Similarly a large CSI of about 100 amino acids in RpoB homologs (between amino acids 919-1058) is present in various species belonging to Pseudomonadota, Bacteroidota , Chlorobiota , Chlamydiota , Planctomycetota, and Aquificota. This CSI is absent in other ancestral bacterial phyla as well as Archaea. In both cases one can infer that

1200-437: Is itself a chordate, and that craniates ' nearest relatives are tunicates. Recent identification of two conserved signature indels (CSIs) in the proteins cyclophilin-like protein and mitochondrial inner membrane protease ATP23, which are exclusively shared by all vertebrates , tunicates and cephalochordates also provide strong evidence of the monophyly of Chordata. All of the earliest chordate fossils have been found in

1260-423: Is not yet settled. A specific relationship between Vertebrates and Tunicates is also strongly supported by two CSIs found in the proteins predicted exosome complex RRP44 and serine palmitoyltransferase, that are exclusively shared by species from these two subphyla but not Cephalochordates , indicating Vertebrates are more closely related to Tunicates than Cephalochordates . Below is a phylogenetic tree of

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1320-574: The echinoderms (whose modern members include starfish , sea urchins and crinoids ), are quite common from the start of the Cambrian, 542  million years ago . The Mid Cambrian fossil Rhabdotubus johanssoni has been interpreted as a pterobranch hemichordate. Opinions differ about whether the Chengjiang fauna fossil Yunnanozoon , from the earlier Cambrian, was a hemichordate or chordate. Another fossil, Haikouella lanceolata , also from

1380-412: The echinoderms , and together they form the clade Ambulacraria , the sister phylum of the chordates. Chordata, Ambulacraria, and possibly Xenacoelomorpha are believed to form the superphylum Deuterostomia , although this has recently been called into doubt. Chordata is the third-largest phylum of the animal kingdom (behind only the protostomal phyla Arthropoda and Mollusca ) and is also one of

1440-459: The notochord is replaced by the vertebral column . It consists of a series of bony or cartilaginous cylindrical vertebrae, generally with neural arches that protect the spinal cord , and with projections that link the vertebrae. Hagfishes have incomplete braincases and no vertebrae, and are therefore not regarded as vertebrates, but they are members of the craniates, the group within which vertebrates are thought to have evolved . However

1500-463: The Chengjiang fauna, is interpreted as a chordate and possibly a craniate, as it shows signs of a heart, arteries, gill filaments, a tail, a neural chord with a brain at the front end, and possibly eyes—although it also had short tentacles round its mouth. Haikouichthys and Myllokunmingia , also from the Chengjiang fauna, are regarded as fish . Pikaia , discovered much earlier (1911) but from

1560-483: The Early Cambrian Chengjiang fauna , and include two species that are regarded as fish , which implies that they are vertebrates. Because the fossil record of early chordates is poor, only molecular phylogenetics offers a reasonable prospect of dating their emergence. However, the use of molecular phylogenetics for dating evolutionary transitions is controversial. It has also proved difficult to produce

1620-647: The Mid Cambrian Burgess Shale (505 Ma), is also regarded as a primitive chordate. On the other hand, fossils of early chordates are very rare, since invertebrate chordates have no bones or teeth, and only one has been reported for the rest of the Cambrian. The best known and earliest unequivocally identified Tunicate is Shankouclava shankouense from the Lower Cambrian Maotianshan Shale at Shankou village, Anning, near Kunming ( South China ). The evolutionary relationships between

1680-478: The aid of a net of mucus slowly pulled across the slits by cilia . Doliolids and salps alternate between asexual and sexual life stages. Salp colonies can be several meters in length. Doliolids and salps rely on muscular action to propel themselves through surrounding seawater. Thaliaceans have complex lifecycles. Doliolid eggs hatch into swimming tadpole larvae, which are the common larval stage for other urochordates . Pyrosomes are ovoviviparous , meaning

1740-408: The body consists of the large pharynx . Water enters the pharynx through the large buccal siphon at the front end of the animal, and is forced through a number of slits in the pharyngeal wall into an atrium lying just behind it. From here, the water is expelled through an atrial siphon at the posterior end. The pharynx is both a respiratory organ and a digestive one, filtering food from the water with

1800-435: The chordate groups and between chordates as a whole and their closest deuterostome relatives have been debated since 1890. Studies based on anatomical, embryological , and paleontological data have produced different "family trees". Some closely linked chordates and hemichordates, but that idea is now rejected. Combining such analyses with data from a small set of ribosome RNA genes eliminated some older ideas, but opened up

1860-568: The cladistic exclusion of hagfish from the vertebrates is controversial, as they may instead be degenerate vertebrates who have secondarily lost their vertebral columns. The position of lampreys is ambiguous. They have complete braincases and rudimentary vertebrae, and therefore may be regarded as vertebrates and true fish . However, molecular phylogenetics , which uses biochemical features to classify organisms, has produced both results that group them with vertebrates and others that group them with hagfish. If lampreys are more closely related to

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1920-593: The class Gammaproteobacteria. A 2 aa deletion in AICAR transformylase was uniquely shared by all gammaproteobacteria except for Francisella tularensis . A 4 aa deletion in RNA polymerase b-subunit and a 1 aa deletion in ribosomal protein L16 were found uniquely in various species belonging to the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales, but were not found in other gammaproteobacteria. Lastly,

1980-718: The class or its different subgroups are known. A detailed CSI-based study was conducted to better understand the phylogeny of this class. Firstly, a phylogenetic tree based on concatenated sequences of a number of universally-distributed proteins was created. The branching order of the different orders of the class Gammaproteobacteria (from most recent to the earliest diverging) was: Enterobacteriales > Pasteurellales > Vibrionales , Aeromonadales > Alteromonadales > Oceanospirillales , Pseudomonadales > Chromatiales , Legionellales , Methylococcales , Xanthomonadales , Cardiobacteriales , Thiotrichales . Additionally, 4 CSIs were discovered that were unique to most species of

2040-470: The classification of chordates. Some chordate lineages may only be found by DNA analysis, when there is no physical trace of any chordate-like structures. Attempts to work out the evolutionary relationships of the chordates have produced several hypotheses. The current consensus is that chordates are monophyletic , meaning that the Chordata include all and only the descendants of a single common ancestor, which

2100-429: The discovery and analyses of conserved indels (CSIs) in many universally distributed proteins have aided in this quest. The genetic events leading to them are postulated to have occurred at important evolutionary branch points and their species distribution patterns provide valuable information regarding the branching order and interrelationships among different bacterial phyla. Recently the phylogenetic relationship of

2160-534: The earliest-branching chordate subphylum. The tunicates have three distinct adult shapes. Each is a member of one of three monophylitic clades. All tunicate larvae have the standard chordate features, including long, tadpole -like tails. Their larva also have rudimentary brains, light sensors and tilt sensors. The smallest of the three groups of tunicates is the Appendicularia . They retain tadpole-like shapes and active swimming all their lives, and were for

2220-549: The eggs develop inside the "mother" without the tadpole stage. Salps are viviparous , meaning the embryos are linked to the "mother" by a placenta. This then develops into an oozoid, which reproduces asexually by budding to produce a number of blastozoids , which form long chains (see image). The individual blastozoids then reproduce sexually to produce the eggs and the next generation of oozoids. The dorsal, hollow nerve cord and notochord found in Chordata has been lost, except for

2280-408: The first of these synapomorphies, the notochord, which plays a significant role in chordate body plan structuring and movements. Chordates are also bilaterally symmetric , have a coelom , possess a closed circulatory system , and exhibit metameric segmentation . Although the name Chordata is attributed to William Bateson (1885), it was already in prevalent use by 1880. Ernst Haeckel described

2340-651: The formal definition: The following schema is from the 2015 edition of Vertebrate Palaeontology . The invertebrate chordate classes are from Fishes of the World . While it is structured so as to reflect evolutionary relationships (similar to a cladogram ), it also retains the traditional ranks used in Linnaean taxonomy . Cephalochordates , one of the three subdivisions of chordates, are small, "vaguely fish-shaped" animals that lack brains, clearly defined heads and specialized sense organs. These burrowing filter-feeders compose

2400-426: The fossil record, and their assumption that the molecular clock runs at a known constant rate has been challenged. Traditionally, Cephalochordata and Craniata were grouped into the proposed clade "Euchordata", which would have been the sister group to Tunicata/Urochordata. More recently, Cephalochordata has been thought of as a sister group to the "Olfactores", which includes the craniates and tunicates. The matter

2460-479: The group Thermotogota was characterized based on the CSI approach. Previously no biochemical or molecular markers were known that could clearly distinguish the species of this phylum from all other bacteria. More than 60 CSIs that were specific for the entire Thermotogota phylum or its different subgroups were discovered. Of these, 18 CSIs are uniquely present in various Thermotogota species and provide molecular markers for

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2520-418: The groups lacking the CSI are ancestral. A key issue in bacterial phylogeny is to understand how different bacterial species are related to each other and their branching order from a common ancestor. Currently most phylogenetic trees are based on 16S rRNA or other genes/proteins. These trees are not always able to resolve key phylogenetic questions with a high degree of certainty. However in recent years

2580-462: The hagfish than the other vertebrates, this would suggest that they form a clade , which has been named the Cyclostomata . There is still much ongoing differential (DNA sequence based) comparison research that is trying to separate out the simplest forms of chordates. As some lineages of the 90% of species that lack a backbone or notochord might have lost these structures over time, this complicates

2640-454: The indel is an insert or a deletion, and which of these two groups A, B, C or X, Y, Z is ancestral. Mainline CSIs have been used in the past to determine the phylogenetic relationship of a number of bacterial phyla. The large CSI of about 150-180 amino acids within a conserved region of Gyrase B (between amino acids 529-751), is commonly shared between various Pseudomonadota , Chlamydiota , Planctomycetota and Aquificota species. This CSI

2700-503: The interpretation of a CSI. By determining the presence or absence of CSIs in an out-group species, one can infer whether the ancestral form of the CSI was an insert or deletion and this can be used to develop a rooted phylogenetic relationship among organisms. CSIs are discovered by looking for shared changes in a phylogenetic tree constructed from protein sequences. Most CSIs that have been identified have been found to have high predictive value upon addition of new sequences, retaining

2760-485: The most ancient taxons. Chordate fossils have been found from as early as the Cambrian explosion over 539 million years ago. Of the more than 81,000 living species of chordates, about half are ray-finned fishes ( class Actinopterygii ) and the vast majority of the rest are tetrapods , a terrestrial clade of lobe-finned fishes ( Sarcopterygii ) who evolved air-breathing using lungs . The name "chordate" comes from

2820-533: The number of CSIs that are commonly shared with other taxa is much smaller than those that are specific for Thermotogota and they do not exhibit any specific pattern. Hence they have no significant effect on the distinction of Thermotogota. Mesophillic Thermoproteota were recently placed into a new phylum of Archaea called the Nitrososphaerota (formerly Thaumarchaeota). However there are very few molecular markers that can distinguish this group of archaea from

2880-430: The order Pasteurellales are currently distinguished mainly based on their position in the branching of the 16srRNA tree. There are currently very few molecular markers known that can distinguish members of this order from other bacteria. A CSI approach was recently used to elucidate the phylogenetic relationships between the species in this order; more than 40 CSIs were discovered that were uniquely shared by all or most of

2940-682: The past to determine the phylogenetic relationship of a number of bacterial phyla and subgroups within it. For example a 3 amino acid insert was uniquely shared by members of the phylum Thermotogota (formerly Thermotogae) in the essential 50S ribosomal protein L7/L12 , within a highly conserved region (82-124 amino acid). This is not present in any other bacteria species and could be used to characterize members of Thermotogota from all other bacteria. Group-specific CSIs were also used to characterize subgroups within Thermotogota. Mainline CSIs are those in which

3000-458: The phylum Thermoproteota (formerly Crenarchaeota). A detailed phylogenetic study using the CSI approach was conducted to distinguish these phyla in molecular terms. 6 CSIs were uniquely found in various Nitrososphaerota, namely Cenarchaeum symbiosum , Nitrosopumilus maritimus and a number of uncultured marine Thermoproteota. 3 CSIs were found that were commonly shared between species belonging to Nitrososphaerota and Thermoproteota. Additionally,

3060-815: The phylum. Additionally there were many CSIs that were specific for various Thermotogota subgroups. Another 12 CSIs were specific for a clade consisting of various Thermotogota species except Tt. Lettingae. While 14 CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and 18 CSIs were specific for the genus Thermosiphon . Lastly 16 CSIs were reported that were shared by either some or all Thermotogota species or some species from other taxa such as Archaea , Aquificota , Bacillota , Pseudomonadota , Deinococcota , Fusobacteriota , Dictyoglomota , Chloroflexota , and eukaryotes . The shared presence of some of these CSIs could be due to lateral gene transfer (LGT) between these groups. However

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3120-748: The phylum. Lines of the cladogram show probable evolutionary relationships between both extinct taxa, which are denoted with a dagger (†), and extant taxa . Cephalochordata (lancelets) [REDACTED] Appendicularia (larvaceans) [REDACTED] Thaliacea [REDACTED] Phlebobranchia [REDACTED] Aplousobranchia [REDACTED] Stolidobranchia [REDACTED] Myllokunmingiida † [REDACTED] Anaspidomorphi † [REDACTED] Conodonta † [REDACTED] Myxini (hagfish) [REDACTED] Hyperoartia (lampreys) [REDACTED] Pteraspidomorphi † [REDACTED] Thelodonti † [REDACTED] Conserved signature indels The CSIs that are restricted to

3180-409: The possibility that tunicates (urochordates) are "basal deuterostomes", surviving members of the group from which echinoderms, hemichordates and chordates evolved. Some researchers believe that, within the chordates, craniates are most closely related to cephalochordates, but there are also reasons for regarding tunicates (urochordates) as craniates' closest relatives. Since early chordates have left

3240-410: The sea floor, where they remain in one place for life, feeding on plankton. The salps float in mid-water, feeding on plankton , and have a two-generation cycle in which one generation is solitary and the next forms chain-like colonies . The etymology of the term Urochordata (Balfour 1881) is from the ancient Greek οὐρά (oura, "tail") + Latin chorda ("cord"), because the notochord is only found in

3300-431: The species. Two major clades are formed within this Pasteurellales: Clade I, encompassing Aggregatibacter , Pasteurella , Actinobacillus succinogenes , Mannheimia succiniciproducens , Haemophilus influenzae and Haemophilus somnus , was supported by 13 CSIs. Clade II, encompassing Actinobacillus pleuropneumoniae , Actinobacillus minor , Haemophilus ducreyi , Mannheimia haemolytica and Haemophilus parasuis ,

3360-434: The specificity for the originally identified clades of species. They can be used to identify both known and even previously unknown species belonging to these groups in different environments. Compared to tree branching orders which can vary among methods, specific CSIs make for more concrete circumscriptions that are computationally cheaper to apply. Group-specific CSIs are commonly shared by different species belonging to

3420-578: The start of the Cambrian 538.8  million years ago . Three enigmatic species that are possible very early tunicates, and therefor deuterostomes, were also found from the Ediacaran period – Ausia fenestrata from the Nama Group of Namibia , the sac-like Yarnemia ascidiformis , and one from a second new Ausia -like genus from the Onega Peninsula of northern Russia , Burykhia hunti . Results of

3480-408: The tail. The term Tunicata (Lamarck 1816) is recognised as having precedence and is now more commonly used. Craniates all have distinct skulls . They include the hagfish , which have no vertebrae . Michael J. Benton commented that "craniates are characterized by their heads, just as chordates, or possibly all deuterostomes , are by their tails". Most craniates are vertebrates , in which

3540-494: The taxon X. This is a distinctive characteristic of this taxon as it is not found in any other species. This signature was likely introduced in a common ancestor of the species from this taxon. Similarly other group-specific signatures (not shown) could be shared by either A1 and A2 or B1 and B2, etc., or even by X1 and X2 or by X3 and X4, etc. The groups A, B, C, D and X, in this diagram could correspond to various bacterial or Eukaryotic phyla. Group-specific CSIs have been used in

3600-481: Was supported by 9 CSIs. Based on these results, it was proposed that Pasteurellales be divided from its current one family into two different ones. Additionally, the signatures described would provide novel means of identifying undiscovered Pasteurellales species. The class Gammaproteobacteria forms one of the largest groups of bacteria. It is currently distinguished from other bacteria solely by 16s rRNA -based phylogenetic trees. No molecular characteristics unique to

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